Ah, so if I add several files in a batch, they'll be represented as a single item in the queue, and then "yes to all" applies to all the files within that single queue item.

In which case, yes, a "yes to all" for the entire queue would be great, because often I queue some files with dependencies that I need to replace, and I want them all replaced as quickly as possible to avoid the live site being in a broken state any longer than necessary.

I have voted, but now see that you have quite a list of requests to work through that appear to be a higher priority! Good luck, and thank you!

Indeed, the "Yes to All" works for that one queue entry only. So if the entry is just one file, it has no effect.
The "never ask again" is permanent.

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I have added this to the tracker:
Issue 2464 – Option to confirm overwriting for all files in queue
You can vote for it there.

Perhaps I'm missing something, but whenever I queue several files "in background", and then start the queue processing, I get the expected "Overwrite?" modal but the "Yes to All" dropdown option never seems to do anything different to "Yes". I have to do it for every file. There's a checkbox to "never ask again", but unlike Filezilla, it's not clear if that'll apply to all future transfers, or just the current queue. An explicit option would be welcome, but if "Yes to All" worked intuitively for the current queue, that would be good.